Genetically modifiedand uses thereof

The present application is a National Stage Application claiming priority from co-pending PCT Application No. PCT/US2020/016522 filed Feb. 4, 2020, which in turn claims benefit of priority to U.S. Provisional Application Ser. No. 62/801,307, filed Feb. 5, 2019, all of which are is hereby incorporated by reference in their its entirety.

The present invention relates to a live delivery platform, such as a genetically modified bacterium, to deliver preventative or therapeutic anti-infective activity, immunomodulatory factors, or growth-promoting biomolecules directly to the mucosa of an animal in need thereof.

Direct fed microbials (DFMs), often also called probiotics, are microorganisms which colonize the gastrointestinal tract of an animal and provide some beneficial effect to that animal. The microorganisms can be bacterial species, for example those from the genera, and. The microorganisms can also be yeast or even molds. The microorganisms can be provided to an animal orally or mucosally or, in the case of birds, provided to a fertilized egg, i.e. in ovo.

The beneficial activity provided by a DFM can be the synthesis of vitamins or other nutritional molecules needed for a healthy metabolism of the host animal. A DFM can also protect the host animal from disease, disorders, or clinical symptoms caused by other, pathogenic microorganisms. For example, the DFM may naturally produce factors having inhibitory or cytotoxic activity against certain species of pathogens, such as deleterious or disease-causing bacteria. However, the DFM may not be able to produce such factors in sufficient quantity to reduce infection of the host with the pathogen, or the factors may affect only a limited set of pathogens, leaving the host vulnerable to other pathogens.

Stronger or more broad-based antibiotics can be administered to the host animal, for example orally or parenterally, but these would have a limited duration in the host, and thus may require repeated administration. Oral delivery may also result in the degradation of the antibiotics or failure to deliver the antibiotic to the particular anatomical site where the therapeutic effect is most needed. Development of antibiotic resistance by pathogens is another important concern.

What is needed is a delivery system which can constantly deliver anti-infective molecules directly to the gastrointestinal or respiratory tract where pathogenic bacteria are replicating in the host. The gastrointestinal and respiratory systems are also often a point of entry of the pathogen into the host. Preferably, the delivery system is a live genetically modified microorganism, such as a bacterium, which can colonize the gastrointestinal or respiratory tract of a host and directly deliver antibiotic factors to reduce the number of, or block the entry of, a pathogen. For example, in ovo delivery of a live delivery platform could prevent early colonization of an embryo by pathogens, possibly through competitive exclusion or direct or indirect anti-infective effects. In ovo delivery has the further advantage of bypassing any limitations of colonization by the genetically-modified microorganism due to maternal antibody interference. Preferably, the live bacterial delivery system synthesizes the anti-infective factor in sufficient quantity to have the desired effect on a pathogen. A targeted pathogen may be, without limitation, a bacterium of the genera, or, or anbacterium, or a parasite such as anspecies. Preferably, the live bacterial system persists in the host gastrointestinal tract for a period of time. Preferably, the live bacterial delivery system produces a broad-spectrum anti-infective factor or multiple anti-infective factors, such that a variety of pathogens are targeted. Alternatively, a combination of live delivery systems could be administered to a single animal, with genetically modified bacteria producing multiple anti-infective factors, immunomodulatory molecules, or growth-promoting biomolecules, or any combination thereof. Thus, more than one disease state is prevented or reduced, or diseases and syndromes having multiple causes can be effectively treated.

Provided herein is disclosure of anti-infective peptides, including new mersacidin-like peptides, which target multiple bacterial species. Also disclosed are antibodies, including single chain antibodies, which target specific pathogens and pathogenic molecules. Also disclosed are phage or phage lytic peptides which target pathogenic species. Provided also is aexpression system which can produce high levels of at least one or a multiplicity of the above molecules, preferably as surface-displayed or secreted molecules.

The present invention provides a live delivery platform comprising a genetically modified microorganism. The genetically modified microorganism comprises an expression cassette containing one or more of: a promoter for transcriptional expression, a nucleic acid sequence encoding a signal sequence for secretion, a nucleic acid sequence encoding a cell-wall anchor, at least one heterologous coding region encoding a desired biomolecule, a nucleic acid sequence encoding an expressed peptide tag for detection, and terminators for translation and transcription termination. The genetically modified microorganism may be a bacterium, a yeast, or a fungus. A genetically modified bacterium is preferably a, or an. The genetically modified bacterium may also preferably be anbacterium. The genetically modified bacterium may also preferably be astrain. The present invention provides an expression cassette within a genetically modified microorganism that may include a promoter for transcriptional expression. The promoter for transcriptional expression may comprise a nucleic acid sequence of SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 41, SEQ ID NO: 42, and SEQ ID NO: 43.

The present invention provides an expression cassette within a genetically modified microorganism that may include a nucleic acid sequence encoding a signal sequence for secretion. The signal sequence for secretion may be at least 20 amino acids, at least 25 amino acids, at least 30 amino acids, at least 35 amino acids, at least 40 amino acids, at least 44 amino acids, at least 50 amino acids, at least 55 amino acids, at least 60 amino acids, or at least 65 amino acids. The signal sequence for secretion may also be 20-65 amino acids, 20-60 amino acids; 20-55 amino acids; 20-50 amino acids, 20-45 amino acids, 20-40 amino acids, 20-35 amino acids, 20-30 amino acids, 25-65 amino acids, 25-60 amino acids; 25-55 amino acids; 25-50 amino acids, 25-45 amino acids, 25-40 amino acids, 25-35 amino acids, 25-30 amino acids, 30-65 amino acids, 30-60 amino acids; 30-55 amino acids; 30-50 amino acids, 30-45 amino acids, 30-40 amino acids, or 30-35 amino acids. The signal sequence for secretion may comprise an amino acid sequence that is a fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein. The signal sequence for secretion may comprise an amino acid sequence that is an amino-terminal fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein.

The present invention provides an expression cassette within a genetically modified microorganism that may include a nucleic acid sequence encoding a cell wall anchor peptide. The cell wall anchor peptide may have a length of 100-250 amino acids, 100-225 amino acids, 100-200 amino acids, 100-175 amino acids, 100-150 amino acids, 125-250 amino acids, 125-225 amino acids, 125-200 amino acids, 125-175 amino acids, or 125-150 amino acids. The cell wall anchor may comprise an amino acid sequence that is a fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein. The cell wall anchor may comprise an amino acid sequence that is a carboxy-terminal fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein.

The present invention provides an expression cassette within a genetically modified microorganism that includes a heterologous coding region encoding a desired biomolecule. The desired biomolecule may be a biomolecule having anti-infective activity, a probiotic factor, an immunomodulatory factor, or a growth-promoting biomolecule. The biomolecule may have anti-infective activity active against a pathogenic bacterium or a parasite. The parasite may preferably be anspecies. The pathogenic bacterium may preferably be a, and anbacterium.

The present invention provides an expression cassette within a genetically modified microorganism that includes a heterologous coding region encoding a desired biomolecule having anti-infective activity. The anti-infective biomolecule may be a bactericidal peptide, an enzyme, a lysin, a phage, or an antibody. The bactericidal peptide may be a mersacidin-like molecule. The mersacidin-like molecule may comprise a sequence disclosed herein as SEQ ID NO: 2 or SEQ ID NO: 4. The desired biomolecule may be an enzyme. The enzyme may comprise a sequence disclosed herein as SEQ ID NO: 5 or SEQ ID NO: 6. The desired biomolecule may be a lysin. The lysin may comprise a sequence disclosed herein as SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, or SEQ ID NO: 28. The desired biomolecule may be a phage, or a phage in a pro-phage form. The phage genetic material may comprise a sequence disclosed herein as SEQ ID NO: 11, SEQ ID NO: 12, or SEQ ID NO: 13. The desired biomolecule may be derived from aspecies. The desired biomolecule may be abacteriocin. Aanti-infective molecule may comprise a sequence disclosed herein as SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, or SEQ ID NO: 48.

The present invention provides an expression cassette within a genetically modified microorganism that includes a heterologous coding region encoding a desired biomolecule that is an antibody. The antibody may be a single chain antibody. The single chain antibody may be from a camelid. The single chain antibody may specifically recognize a pathogenic microorganism or a molecule produced by a pathogen. The single chain antibody may specifically recognize a bacterial protein, such as for example a toxin or an attachment molecule. The single chain antibody may specifically recognize a bacterial protein from. The bacterial protein may be a protein produced by. The bacterial protein may bealpha toxin orNetB toxin.

The present invention provides an expression cassette within a genetically modified microorganism that includes a heterologous coding region encoding a desired biomolecule that is an antibody that recognizesalpha toxin orNetB toxin. The single chain antibody may comprise an amino acid sequence as disclosed herein as SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 33, or SEQ ID NO: 34.

The present invention provides an expression cassette within a genetically modified microorganism that includes a heterologous coding region encoding a desired biomolecule that is a probiotic factor. The probiotic factor may be an agglutinin receptor. The agglutinin receptor may comprise a sequence disclosed herein as SEQ ID NO: 9 or SEQ ID NO: 10.

The present invention provides a genetically modified microorganism comprising an expression cassette. The expression cassette may comprise a promoter for transcriptional expression, and at least one heterologous coding region encoding a desired biomolecule. The expression cassette may also optionally comprise one or more of a nucleic acid sequence encoding a signal sequence for secretion, a nucleic acid sequence encoding a cell-wall anchor, a nucleic acid sequence encoding an expressed peptide tag for detection, and terminators for translation and transcription termination. The expression cassette may comprise a promoter having a sequence disclosed herein as SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 41, SEQ ID NO: 42, or SEQ ID NO: 43. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule such as a bactericidal peptide, an enzyme, a lysin, a phage, and an antibody. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having anti-infective activity. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having a sequence disclosed herein as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO:34, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, or SEQ ID NO: 50.

The present invention provides a genetically modified microorganism comprising an expression cassette, where the genetically modified bacterium is a, or an. The genetically modified bacterium may be astrain.

The present invention provides a genetically modified microorganism comprising an expression cassette, where the expression cassette is located on a plasmid. The plasmid may comprise a sequence disclosed herein as SEQ ID NO: 8. The present invention provides a genetically-modified microorganism comprising an expression cassette, where the expression cassette is located on a bacterial chromosome. The expression cassette located on a bacterial chromosome may be inserted into a transposase locus. The expression cassette located on a bacterial chromosome may be inserted into an Uracil phosphoribosyl (UPP) transferase locus. The expression cassette located on a bacterial chromosome may be inserted into a pyrE locus.

The present invention provides a method of reducing colonization of an animal by a pathogenic bacterium. The method may comprise treating an animal in need thereof with a live delivery platform. The live delivery platform comprises a genetically modified microorganism. The genetically modified microorganism comprises an expression cassette containing one or more of: a promoter for transcriptional expression, a nucleic acid sequence encoding a signal sequence for secretion, a nucleic acid sequence encoding a cell-wall anchor, at least one heterologous coding region encoding a desired biomolecule, a nucleic acid sequence encoding an expressed peptide tag for detection, and terminators for translation and transcription termination. The genetically modified microorganism may be a bacterium, a yeast, or a fungus. A genetically modified bacterium is preferably a, or an. The genetically modified bacterium may also preferably be anbacterium. The genetically modified bacterium may also preferably be astrain.

The present invention provides a method of reducing colonization of an animal by a pathogenic bacterium, where the method comprises treating an animal in need thereof with a genetically modified microorganism. The genetically modified microorganism is modified to contain an expression cassette. The expression cassette may comprise a promoter for transcriptional expression having a sequence disclosed herein as SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 41, SEQ ID NO: 42, or SEQ ID NO: 43. The expression cassette may further comprise a signal sequence for secretion having an amino acid sequence that is a fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein. A signal sequence for secretion may comprise an amino acid sequence that is an amino-terminal fragment of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 40, where the fragment has a length as given herein. The expression cassette preferably also includes a heterologous coding region encoding a desired biomolecule. The desired biomolecule may be a biomolecule having anti-infective activity, a probiotic factor, an immunomodulatory factor, or a growth-promoting biomolecule. The biomolecule may have anti-infective activity active against a pathogenic bacterium or a parasite. The parasite may preferably be anspecies. The pathogenic bacterium may preferably be a, and anbacterium. The anti-infective biomolecule may be a bactericidal peptide, an enzyme, a lysin, a phage, or an antibody. The expression cassette may optionally contain a nucleic acid sequence encoding a cell-wall anchor, a nucleic acid sequence encoding an expressed peptide tag for detection, and/or terminators for translation and transcription termination.

The present invention provides a method of reducing colonization of an animal by a pathogenic bacterium, where the method comprises treating an animal in need thereof with a genetically modified microorganism. The animal may be a bird, a human, or a non-human mammal. The treatment may be administered orally, parentally, nasally, or mucosally. When the animal is a bird the treatment may be administered in ovo.

The present invention provides a use of any genetically modified microorganism disclosed herein in therapy. The present invention provides a use in therapy of a bacterium genetically modified to contain any expression cassette as disclosed herein. A therapy may be reducing colonization of an animal by a pathogenic bacterium.

The present invention provides a use of any expression cassette disclosed herein in therapy. The present invention provides a use in therapy of any expression cassette as disclosed herein. A therapy may be reducing colonization of an animal by a pathogenic bacterium. The expression cassette should comprise at least one heterologous coding region encoding a desired biomolecule. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule such as a bactericidal peptide, an enzyme, a lysin, a phage, and an antibody. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having anti-infective activity. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having a sequence disclosed herein as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO:34, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, or SEQ ID NO: 50.

The present invention provides a use of any genetically modified microorganism disclosed herein in the manufacture of a medicament for reducing colonization of an animal by a pathogenic bacterium. The present invention provides for use of a bacterium genetically modified to contain any expression cassette as disclosed herein in the manufacture of a medicament for reducing colonization of an animal by a pathogenic bacterium.

The present invention provides a use of any expression cassette disclosed herein in the manufacture of a medicament for reducing colonization of an animal by a pathogenic bacterium. The present invention provides a use in manufacture of a medicament of any expression cassette as disclosed herein. The medicament may be for reducing colonization of an animal by a pathogenic bacterium. The expression cassette should comprise at least one heterologous coding region encoding a desired biomolecule. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule such as a bactericidal peptide, an enzyme, a lysin, a phage, and an antibody. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having anti-infective activity. The at least one heterologous coding region encoding a desired biomolecule may encode a biomolecule having a sequence disclosed herein as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO:34, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, or SEQ ID NO: 50.

The present invention provides an antibody comprising an amino acid sequence of SEQ ID NO: 29, SEQ ID NO: 49, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 50 or SEQ ID NO: 34. The antibody preferably binds a toxin produced by. The antibody preferably bindsalpha toxin or aNetB toxin. The present invention provides use of an antibody comprising an amino acid sequence of SEQ ID NO: 29, SEQ ID NO: 49, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 50 or SEQ ID NO: 34 in therapy. The present invention provides use of an antibody comprising an amino acid sequence of SEQ ID NO: 29, SEQ ID NO: 49, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 50 or SEQ ID NO: 34 in reducing colonization of an animal by abacterium. The present invention provides use of an antibody comprising an amino acid sequence of SEQ ID NO: 29, SEQ ID NO: 49, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 50 or SEQ ID NO: 34 in the manufacture of medicament to reduce colonization of an animal by abacterium. The present invention provides a method of treating an animal forinfection or colonization, where the method comprises administering an antibody comprising an amino acid sequence of SEQ ID NO: 29, SEQ ID NO: 49, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 50 or SEQ ID NO: 34 to an animal in need thereof.

As used herein, a “genetically-modified microorganism” means any microorganism which has been altered from the natural state using molecular biological techniques. A genetic modification could be the deletion of a portion of the bacterial chromosome or a naturally-occurring plasmid. The genetic modification could also be the introduction of an artificial or exogenous nucleic acid into a portion of the chromosome. The introduction may or may not disturb or perturb the expression of a bacterial gene. The genetic modification could also be the introduction of an artificial plasmid. The genetically-modified microorganism may be a bacterium, a virus, a yeast, a mold, or a single-celled organism.

An “artificial nucleic acid” or “artificial plasmid” is any nucleic acid or plasmid which does not occur naturally, but rather has been constructed using molecular biological techniques. Portions of the nucleic acid or plasmid may occur naturally, but those portions are in an artificial relationship or organization.

As used herein, an “expression cassette” is an artificial nucleic acid constructed to result in the expression of a desired biomolecule by the genetically-modified microorganism. An expression cassette comprises one or more of a promoter for transcriptional expression, a nucleic acid sequence encoding a signal sequence for secretion, a nucleic acid sequence encoding a cell-wall anchor, at least one heterologous coding region encoding a desired biomolecule, a nucleic acid sequence encoding an expressed peptide tag for detection, and terminators for translation and transcription termination. A promoter directs the initiation of transcription of the coding regions into a messenger RNA and the translation of the mRNA into a peptide. A signal sequence for secretion, or a secretion signal sequence, directs the peptide to be located outside the cell membrane. The extracellular peptide could be a soluble, secreted protein or it may be cell-associated, particularly if the expression cassette contains a cell wall anchor sequence which attaches the extracellular peptide to a bacterial cell wall. An expressed peptide tag is any amino acid sequence which may be recognized by an antibody or other binding protein. The expressed peptide tag may also bind an inorganic substance, such as a six-histidine tag which binds to nickel molecules. Terminators for translation may be a stop codon or a spacer open reading frame containing a stop codon.

As used herein, a “heterologous coding region” is a nucleic acid sequence containing an open reading frame which encodes a peptide. The coding region is heterologous to the associated promoter, meaning the coding region and the promoter are not associated in their natural states.

As used herein, a “protein” is a sequence of amino acids which assumes a three-dimensional structure. A “peptide” can be used interchangeably with protein but may also be a short linear sequence of amino acids without a defined three-dimensional structure.

As used herein, a “desired biomolecule” is any peptide which may be advantageous to a host when administered via a live delivery platform. The desired biomolecule may be a peptide with anti-infective activity, a probiotic factor, an immunomodulatory factor, an anti-antinutritional factor, or a growth-promoting biomolecule. The desired biomolecule may also be an enzyme which produces a substance with anti-infective activity or a probiotic factor such as a vitamin.

As used herein, “anti-infective activity” includes any activity which prevents infection of a host with a pathogenic organism. The following molecules are examples of biomolecules possessing anti-infective activity: an antibacterial peptide; a lysin or lytic enzyme; a prophage, phage or virus; an enzyme, for example one that cleaves or disables a protein made by a pathogen; and an antibody which blocks, inhibits, or clears a pathogenic molecule. An anti-infective may have bacteriostatic activity, which slows, reduces, or prevents the growth of a pathogenic species. A non-limiting example of an antibacterial peptide is a member of the mersacidin family or a mersacidin-like molecule, such as those described in EP0700998. A non-limiting example of lysins are lytic molecules produced by phage. Lysins may have specificity for certain pathogenic species of bacteria and have been suggested for use in substitution for traditional antibiotics. V. A. Fischetti,, vol. 10, no. 310 (2018); and R. Vazquez et al., vol. 9, article 2252 (2018).

As used herein, a “probiotic factor” is a substance which, when produced by a genetically-modified microorganism, proves beneficial to a host. The probiotic factor may be an attachment molecule or an agglutinizing molecule which promotes colonization of the host with the genetically modified microorganism and/or prolongs the period of time where the genetically modified microorganism colonizes the host. The longer the genetically-modified microorganism persists in the host the longer the beneficial effect is provided.

As used herein, an “immunomodulatory factor” could be a cytokine, lymphokine, chemokine, interleukin, interferon, a colony stimulating factor, or a growth factor. The immunomodulatory factor could provide nonspecific enhancement of an immune response or the immunomodulatory factor could increase the number or tissue distribution of immune cells present in the host. The immunomodulatory factor may also reduce an inappropriate immune response, such as without limitation an autoimmune response.

As used herein, a “growth-promoting biomolecule” could be a growth factor, a transfer factor (such as an iron-chelating molecule), a hormone, or any other factor which promotes healthy metabolic activity.

As used herein, an “anti-nutritional factor” could include protease inhibitors, for example a trypsin inhibitor.

As used herein, “delivery” or “administration” means the act of providing a beneficial activity to a host. The delivery may be direct or indirect. An administration could be by an oral, nasal, or mucosal route. For example without limitation, an oral route may be an administration through drinking water, a nasal route of administration may be through a spray or vapor, and a mucosal route of administration may be through direct contact with mucosal tissue. Mucosal tissue is a membrane rich in mucous glands such as those that line the inside surface of the nose, mouth, esophagus, trachea, lungs, stomach, gut, intestines, and anus. In the case of birds, administration may be in ovo, i.e. administration to a fertilized egg. In ovo administration can be via a liquid which is sprayed onto the egg shell surface, or an injected through the shell.

As used herein, the terms “treating”, “to treat”, or “treatment”, include restraining, slowing, stopping, reducing, ameliorating, or reversing the progression or severity of an existing symptom, disorder, condition, or disease. A treatment may also be applied prophylactically to prevent or reduce the incidence, occurrence, risk, or severity of a clinical symptom, disorder, condition, or disease. As used herein, the term “reducing” may apply to both prophylactic (e.g. preventative) treatments or therapeutic treatments.

The following experimental examples are illustrative of a live delivery system comprisingexpression cassettes which can be delivered by the disclosed live delivery platform. It will be appreciated that other embodiments and uses will be apparent to those skilled in the art and that the invention is not limited to these specific illustrative examples or preferred embodiments. The descriptive headings of these Examples are for convenience only and should not influence interpretation of any of the results presented therein.

Seven() strains are isolated from older birds at the Research Center, Hannover from the cecal contents received from the Poultry Clinic, University of Hannover. All the seven strains are identified to beby 16S rRNA sequencing.

While only limited growth is observed for most strains under aerobic conditions in MRS broth and agar (de Man, J. D.; Rogosa, M.; and Sharpe, M. E. “A Medium for the Cultivation of Lactobacilli”.23: 130-135 (1960)), all isolates show very good growth on MRS agar and MRS broth under anaerobic conditions at 39° C. Culturing the bacterial strains on blood agar under anaerobic conditions results mostly in limited growth. None of the strains is able to grow in Mueller Hinton broth under anaerobic conditions. For all further analysis, bacterial strains are grown in MRS medium under anaerobic conditions at 39° C.

Antimicrobial susceptibility of bacterial isolates is tested using the AVIPRO® PLATE (). All strains are resistant against colistin, doxycycline, enrofloxacin, erythromycin, neomycin, oxacillin, penicillin G, trimethroprim-sulfamethoxazole, tetracycline, tilmicosin and tylosin. All strains are resistant to streptomycin except strain 3632, and to tiamulin except strain 2098. In addition, resistance to cefpodaxime-proxetil is observed with strains 2091, 2095, 2097 and 3630; resistance to cefotaxime is observed with strains 2091, 2095 and 2097; and resistance to lincomycin is observed with strainsand. No strain is found to be resistant against amoxicillin, ceftiofur, erythromycin D, lincomycin-spectinomycin and rifampicin under tested concentrations.strain 3632 was deposited on 19 Jun. 2020 according to the Budapest Treaty in the American Type Culture Collection (ATCC), ATCC Patent Depository, 10801 University Boulevard, Manassas, Va., 20110, USA. The deposit was assigned ATCC Patent Deposit Number PTA-126788strain 3630was deposited on 19 Jun. 2020 according to the Budapest Treaty in the American Type Culture Collection (ATCC), ATCC Patent Depository, 10801 University Boulevard, Manassas, Va., 20110, USA. The deposit was assigned ATCC Patent Deposit Number PTA-126787.

To select the best strain for further engineering, theisolates are tested for various desirable probiotic anti-infective properties, such as growth kinetics, ability to produce hydrogen peroxide, auto-aggregation, enzyme profile, survival in the presence of ox bile and pancreatic enzymes, and sensitivity to heat shock and pH changes. Thestrains are also tested for safety using a haemolytic assay.

In general, all strains behave very similar in terms of probiotic properties, including growth kinetics and ability to produce hydrogen peroxide, except for strain 3632, which shows some unique properties, including the ability to auto-aggregate in liquid media (comparable to that of the well-characterized human probiotic strainATCC 23272). None of the strains is found to be hemolytic on blood agar plates, suggesting that these isolates are less likely to be pathogenic to humans.

Whole-genome sequencing is performed forstrains 2091 and 3632, and an independently isolatedstrain 170331 of European origin, using PACBIO® sequencing (Amplicon Express). Sequencing, assembly and annotation statistics are summarized in TABLE 1. Genomic structures and organization differ among the tested strains.

Based on the genome sequencing data, strain 3632 encodes for two bacteriocins belonging to mersacidin family based on homology to the mersacidin conserved domain. These bacteriocins appear to be unique to strain 3632. A cDNA encoding one mersacidin (mersacidin-E1) could be:

(SEQ ID NO: 1). This novel open reading frame would encode a polypeptide of mersacidin-E1: